#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
PTPRC	5788	broad.mit.edu	37	1	198697499	198697499	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr1:198697499C>T	ENST00000367376.2	+	16	1916	c.1745C>T	c.(1744-1746)gCa>gTa	p.A582V	PTPRC_ENST00000352140.3_Missense_Mutation_p.A534V|PTPRC_ENST00000442510.2_Missense_Mutation_p.A584V|PTPRC_ENST00000348564.6_Missense_Mutation_p.A423V|PTPRC_ENST00000594404.1_Missense_Mutation_p.A421V	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	582					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A582V(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						GCATTTCTGGCATTTCTGATT	0.318																																																1	Substitution - Missense(1)	ovary(1)	1											120.0	126.0	124.0					1																	198697499		2202	4299	6501	196964122	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1745C>T	1.37:g.198697499C>T	ENSP00000356346:p.Ala582Val		196964122	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	C	2.627	-0.287192	0.05605	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.02067	4.47	5.47	-3.06	0.05379	.	1.024570	0.07794	N	0.955408	T	0.00906	0.0030	N	0.01228	-0.945	0.19775	N	0.999956	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0	B;B;B;B;B	0.11329	0.006;0.003;0.002;0.002;0.002	T	0.47262	-0.9131	10	0.02654	T	1	.	13.0639	0.59022	0.0:0.4427:0.0:0.5573	.	518;518;423;534;582	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	V	584;518;534;534;468;582;516;421	ENSP00000193532:A534V	ENSP00000306782:A421V	A	+	2	0	PTPRC	196964122	0.002000	0.14202	0.147000	0.22382	0.924000	0.55760	-0.238000	0.08977	-0.470000	0.06901	0.603000	0.83216	GCA		0.318	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
PCDH15	65217	broad.mit.edu	37	10	55566629	55566629	+	Missense_Mutation	SNP	G	G	C			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	C	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr10:55566629G>C	ENST00000373965.2	-	36	5159	c.4765C>G	c.(4765-4767)Cat>Gat	p.H1589D	PCDH15_ENST00000414778.1_Missense_Mutation_p.H1586D	NM_001142771.1|NM_001142772.1	NP_001136243.1|NP_001136244.1	Q96QU1	PCD15_HUMAN	protocadherin-related 15	0					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.H1586D(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTCTCCTCATGTGTCACTGCC	0.483										HNSCC(58;0.16)																																						1	Substitution - Missense(1)	ovary(1)	10											238.0	219.0	225.0					10																	55566629		1568	3582	5150	55236635	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000373965.2:c.4765C>G	10.37:g.55566629G>C	ENSP00000363076:p.His1589Asp		55236635	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000373965.2	37		.	.	.	.	.	.	.	.	.	.	G	15.53	2.861687	0.51482	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746	T;T	0.62105	0.05;0.09	5.86	4.94	0.65067	.	.	.	.	.	T	0.57519	0.2059	L	0.47716	1.5	0.80722	D	1	B;B	0.19583	0.037;0.037	B;B	0.16289	0.015;0.015	T	0.56444	-0.7978	9	0.66056	D	0.02	.	15.773	0.78187	0.0:0.0:0.8626:0.1374	.	1580;1586	C6ZEF7;C9J4F3	.;.	D	1589;1586;1582	ENSP00000363076:H1589D;ENSP00000410304:H1586D	ENSP00000363076:H1589D	H	-	1	0	PCDH15	55236635	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	7.592000	0.82676	1.420000	0.47138	0.655000	0.94253	CAT		0.483	PCDH15-008	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000291336.1	NM_033056	
OR52I1	390037	broad.mit.edu	37	11	4615663	4615663	+	Missense_Mutation	SNP	A	A	G			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr11:4615663A>G	ENST00000530443.2	+	1	395	c.395A>G	c.(394-396)aAg>aGg	p.K132R	OR52I1_ENST00000450052.2_Missense_Mutation_p.K156R	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K157R(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCCATCTGCAAGCCTCTACAC	0.502																																																1	Substitution - Missense(1)	ovary(1)	11											59.0	54.0	56.0					11																	4615663		2201	4295	6496	4572239	SO:0001583	missense	390037			BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"""GPCR / Class A : Olfactory receptors"""	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.395A>G	11.37:g.4615663A>G	ENSP00000436453:p.Lys132Arg		4572239	Q6IF91	Missense_Mutation	SNP	ENST00000530443.2	37	CCDS59223.1	.	.	.	.	.	.	.	.	.	.	A	10.44	1.351904	0.24512	.	.	ENSG00000232268	ENST00000450052;ENST00000530443	T;T	0.00397	7.57;7.57	4.96	3.82	0.43975	GPCR, rhodopsin-like superfamily (1);	0.141770	0.32015	N	0.006711	T	0.00271	0.0008	L	0.35644	1.08	0.26049	N	0.981506	P	0.34800	0.469	B	0.38954	0.286	T	0.55108	-0.8192	9	0.27082	T	0.32	-11.4129	8.9243	0.35630	0.9107:0.0:0.0893:0.0	.	132	Q8NGK6	O52I1_HUMAN	R	156;132	ENSP00000409094:K156R;ENSP00000436453:K132R	ENSP00000409094:K156R	K	+	2	0	OR52I1	4572239	0.000000	0.05858	1.000000	0.80357	0.962000	0.63368	0.495000	0.22483	1.019000	0.39547	0.454000	0.30748	AAG		0.502	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
LRRK2	120892	broad.mit.edu	37	12	40716160	40716160	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr12:40716160C>T	ENST00000298910.7	+	37	5415	c.5357C>T	c.(5356-5358)tCt>tTt	p.S1786F		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1786					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.S1749F(1)|p.S1786F(1)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CACATTGATTCTCTCATGGAA	0.398																																																2	Substitution - Missense(2)	ovary(2)	12											247.0	232.0	237.0					12																	40716160		2203	4300	6503	39002427	SO:0001583	missense	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.5357C>T	12.37:g.40716160C>T	ENSP00000298910:p.Ser1786Phe		39002427	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.769158	0.90020	.	.	ENSG00000188906	ENST00000298910	T	0.75050	-0.9	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.83547	0.5278	L	0.50333	1.59	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71414	0.973;0.965	D	0.83775	0.0222	10	0.56958	D	0.05	.	19.5666	0.95395	0.0:1.0:0.0:0.0	.	1786;1786	Q17RV3;Q5S007	.;LRRK2_HUMAN	F	1786	ENSP00000298910:S1786F	ENSP00000298910:S1786F	S	+	2	0	LRRK2	39002427	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.213000	0.77950	2.602000	0.87976	0.650000	0.86243	TCT		0.398	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
RBM19	9904	broad.mit.edu	37	12	114374899	114374899	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr12:114374899C>T	ENST00000545145.2	-	16	2059	c.1981G>A	c.(1981-1983)Gtc>Atc	p.V661I	RBM19_ENST00000392561.3_Missense_Mutation_p.V661I|RBM19_ENST00000261741.5_Missense_Mutation_p.V661I|RP11-780K2.1_ENST00000550206.1_RNA	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	661					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V661I(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					CTGGAGAAGACGCCAACTGGA	0.537																																																1	Substitution - Missense(1)	ovary(1)	12											122.0	122.0	122.0					12																	114374899		2203	4300	6503	112859282	SO:0001583	missense	9904			AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1981G>A	12.37:g.114374899C>T	ENSP00000442053:p.Val661Ile		112859282	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.537194	0.45176	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05786	3.39;3.39;3.39	4.8	0.89	0.19218	Nucleotide-binding, alpha-beta plait (1);	0.123972	0.53938	D	0.000045	T	0.07279	0.0184	M	0.64404	1.975	0.53688	D	0.999972	B	0.11235	0.004	B	0.14023	0.01	T	0.19910	-1.0291	10	0.27785	T	0.31	-28.0427	9.001	0.36081	0.0:0.6879:0.0:0.3121	.	661	Q9Y4C8	RBM19_HUMAN	I	661	ENSP00000442053:V661I;ENSP00000376344:V661I;ENSP00000261741:V661I	ENSP00000261741:V661I	V	-	1	0	RBM19	112859282	0.870000	0.30015	0.962000	0.40283	0.718000	0.41266	1.624000	0.37018	0.467000	0.27218	0.655000	0.94253	GTC		0.537	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
TCTN2	79867	broad.mit.edu	37	12	124179492	124179492	+	Silent	SNP	T	T	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	T	T	A	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr12:124179492T>A	ENST00000303372.5	+	10	1331	c.1203T>A	c.(1201-1203)atT>atA	p.I401I	TCTN2_ENST00000426174.2_Silent_p.I400I	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	401					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)		p.I401I(1)		breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		ATGTTAAAATTTTTAGGGCAG	0.323																																																1	Substitution - coding silent(1)	ovary(1)	12											42.0	48.0	46.0					12																	124179492		2201	4295	6496	122745445	SO:0001819	synonymous_variant	79867			AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"""Tectonic proteins"""	25774	protein-coding gene	gene with protein product	"""Meckel syndrome, type 8"""	613846	"""chromosome 12 open reading frame 38"""	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.1203T>A	12.37:g.124179492T>A			122745445	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	37	CCDS9253.1																																																																																				0.323	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	
PIBF1	10464	broad.mit.edu	37	13	73428218	73428218	+	Missense_Mutation	SNP	A	A	G			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr13:73428218A>G	ENST00000326291.6	+	10	1585	c.1247A>G	c.(1246-1248)aAt>aGt	p.N416S	AL391384.1_ENST00000408054.1_RNA	NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	416						centrosome (GO:0005813)		p.N416S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		GCAAGGGATAATGCTGTGGCT	0.353																																																1	Substitution - Missense(1)	ovary(1)	13											102.0	105.0	104.0					13																	73428218		2203	4300	6503	72326219	SO:0001583	missense	10464			AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"""progesterone-induced blocking factor 1"""	607532	"""chromosome 13 open reading frame 24"""	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.1247A>G	13.37:g.73428218A>G	ENSP00000317144:p.Asn416Ser		72326219	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Missense_Mutation	SNP	ENST00000326291.6	37	CCDS31991.1	.	.	.	.	.	.	.	.	.	.	A	15.36	2.810460	0.50421	.	.	ENSG00000083535	ENST00000326291	T	0.28255	1.62	5.04	5.04	0.67666	.	0.049112	0.85682	D	0.000000	T	0.50051	0.1593	M	0.69823	2.125	0.49582	D	0.9998	D;D	0.67145	0.996;0.996	D;D	0.73380	0.98;0.98	T	0.47749	-0.9093	10	0.12766	T	0.61	-21.169	13.6217	0.62140	1.0:0.0:0.0:0.0	.	416;416	Q8WXW3;Q4G0R1	PIBF1_HUMAN;.	S	416	ENSP00000317144:N416S	ENSP00000317144:N416S	N	+	2	0	PIBF1	72326219	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	6.247000	0.72411	1.902000	0.55061	0.455000	0.32223	AAT		0.353	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346	
C14orf159	80017	broad.mit.edu	37	14	91691162	91691162	+	Silent	SNP	C	C	T	rs377043453		TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr14:91691162C>T	ENST00000523771.1	+	14	2439	c.1836C>T	c.(1834-1836)acC>acT	p.T612T	C14orf159_ENST00000523576.1_3'UTR|C14orf159_ENST00000522322.1_Silent_p.T612T|C14orf159_ENST00000520328.1_Silent_p.T560T|C14orf159_ENST00000521077.2_Silent_p.T577T|C14orf159_ENST00000428926.2_Silent_p.T612T|C14orf159_ENST00000523816.1_Silent_p.T612T|C14orf159_ENST00000412671.2_Silent_p.T617T|C14orf159_ENST00000518868.1_Silent_p.T617T|C14orf159_ENST00000256324.10_Silent_p.T617T|C14orf159_ENST00000525393.2_Silent_p.T488T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	612						mitochondrion (GO:0005739)		p.T612T(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		TGGACGTCACCACGGCACAGG	0.612																																																1	Substitution - coding silent(1)	ovary(1)	14						C	,,,,	1,4405	2.1+/-5.4	0,1,2202	90.0	64.0	73.0		1836,1836,1851,1680,1836	2.6	0.1	14		73	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,	612/617,612/617,617/622,560/565,612/617	91691162	1,13005	2203	4300	6503	90760915	SO:0001819	synonymous_variant	80017			AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1836C>T	14.37:g.91691162C>T			90760915	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1																																																																																				0.612	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
MTMR10	54893	broad.mit.edu	37	15	31251114	31251114	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr15:31251114C>T	ENST00000435680.1	-	9	984	c.887G>A	c.(886-888)cGa>cAa	p.R296Q	MTMR10_ENST00000563714.1_Missense_Mutation_p.R214Q|RNU6-466P_ENST00000391224.1_RNA|MTMR10_ENST00000314404.8_Missense_Mutation_p.R48Q|MTMR10_ENST00000425768.1_3'UTR	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	296	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)	p.R214Q(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		GAGGGCCATTCGCACAAGAGC	0.458																																																1	Substitution - Missense(1)	ovary(1)	15											144.0	139.0	140.0					15																	31251114		2011	4179	6190	29038406	SO:0001583	missense	54893			AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.887G>A	15.37:g.31251114C>T	ENSP00000402537:p.Arg296Gln		29038406	Q6P4Q6	Missense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	.	.	.	.	.	.	.	.	.	.	C	36	5.603951	0.96626	.	.	ENSG00000166912	ENST00000435680;ENST00000314404;ENST00000340566	D;D	0.98135	-4.74;-4.74	5.08	5.08	0.68730	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.517985	0.20617	N	0.088859	D	0.98732	0.9574	M	0.80982	2.52	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.999;1.0	D;D;D;D	0.87578	0.953;0.996;0.994;0.998	D	0.99887	1.1125	10	0.87932	D	0	.	18.8392	0.92176	0.0:1.0:0.0:0.0	.	65;214;214;296	Q0IJ45;Q9NXD2-2;A6NGL9;Q9NXD2	.;.;.;MTMRA_HUMAN	Q	296;48;214	ENSP00000402537:R296Q;ENSP00000313788:R48Q	ENSP00000313788:R48Q	R	-	2	0	MTMR10	29038406	1.000000	0.71417	0.993000	0.49108	0.968000	0.65278	5.212000	0.65225	2.517000	0.84864	0.655000	0.94253	CGA		0.458	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762	
MAPK6	5597	broad.mit.edu	37	15	52356497	52356497	+	Missense_Mutation	SNP	A	A	C			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	A	A	C	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr15:52356497A>C	ENST00000261845.5	+	6	2273	c.1466A>C	c.(1465-1467)aAg>aCg	p.K489T	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	489					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)	p.K489T(1)		breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		AAATCTGATAAGAAAGGCAAA	0.368																																																1	Substitution - Missense(1)	ovary(1)	15											30.0	30.0	30.0					15																	52356497		2194	4288	6482	50143789	SO:0001583	missense	5597			L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"""Mitogen-activated protein kinase cascade / Kinases"""	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.1466A>C	15.37:g.52356497A>C	ENSP00000261845:p.Lys489Thr		50143789	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	37	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	A	12.03	1.814224	0.32053	.	.	ENSG00000069956	ENST00000261845	T	0.45276	0.9	5.41	5.41	0.78517	.	0.051782	0.85682	D	0.000000	T	0.35913	0.0948	L	0.40543	1.245	0.53688	D	0.999971	P	0.52316	0.952	B	0.39617	0.305	T	0.35251	-0.9796	10	0.72032	D	0.01	-11.4075	15.584	0.76468	1.0:0.0:0.0:0.0	.	489	Q16659	MK06_HUMAN	T	489	ENSP00000261845:K489T	ENSP00000261845:K489T	K	+	2	0	MAPK6	50143789	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.919000	0.70005	2.106000	0.64143	0.519000	0.50382	AAG		0.368	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748	
SV2B	9899	broad.mit.edu	37	15	91809887	91809887	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr15:91809887C>T	ENST00000394232.1	+	7	1554	c.1084C>T	c.(1084-1086)Cgc>Tgc	p.R362C	SV2B_ENST00000545111.2_Missense_Mutation_p.R211C|SV2B_ENST00000330276.4_Missense_Mutation_p.R362C	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	362					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.R362C(1)		NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			CTGGTACCAGCGCTGGCTGGT	0.418																																																1	Substitution - Missense(1)	ovary(1)	15											69.0	69.0	69.0					15																	91809887		2198	4298	6496	89610891	SO:0001583	missense	9899			AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1084C>T	15.37:g.91809887C>T	ENSP00000377779:p.Arg362Cys		89610891	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	C	19.25	3.791225	0.70452	.	.	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.59502	0.26;0.26;0.26	5.44	4.51	0.55191	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.69160	0.3080	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.66716	0.946	T	0.71371	-0.4613	10	0.62326	D	0.03	-22.2555	12.8476	0.57839	0.2956:0.7044:0.0:0.0	.	362	Q7L1I2	SV2B_HUMAN	C	211;362;362	ENSP00000443243:R211C;ENSP00000377779:R362C;ENSP00000332818:R362C	ENSP00000332818:R362C	R	+	1	0	SV2B	89610891	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.163000	0.31798	1.268000	0.44264	0.655000	0.94253	CGC		0.418	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
DNAH3	55567	broad.mit.edu	37	16	21080897	21080897	+	Missense_Mutation	SNP	T	T	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	T	T	A	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr16:21080897T>A	ENST00000261383.3	-	23	3219	c.3220A>T	c.(3220-3222)Att>Ttt	p.I1074F	DNAH3_ENST00000415178.1_Missense_Mutation_p.I1074F	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1074	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.I1074F(1)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TGTATGCGAATTAGCTTTTCT	0.463																																																1	Substitution - Missense(1)	ovary(1)	16											166.0	124.0	139.0					16																	21080897		2201	4300	6501	20988398	SO:0001583	missense	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3220A>T	16.37:g.21080897T>A	ENSP00000261383:p.Ile1074Phe		20988398	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	T	10.70	1.424258	0.25639	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.60920	0.15;0.15	5.4	0.932	0.19466	Dynein heavy chain, domain-2 (1);	0.587686	0.16463	N	0.213311	T	0.46288	0.1385	M	0.71581	2.175	0.09310	N	1	P	0.39480	0.675	B	0.39152	0.292	T	0.30909	-0.9962	10	0.10111	T	0.7	.	2.9451	0.05843	0.117:0.5068:0.1142:0.262	.	1074	Q8TD57	DYH3_HUMAN	F	1074	ENSP00000261383:I1074F;ENSP00000394245:I1074F	ENSP00000261383:I1074F	I	-	1	0	DNAH3	20988398	0.000000	0.05858	0.298000	0.25002	0.721000	0.41392	-0.121000	0.10643	0.313000	0.23062	-0.177000	0.13119	ATT		0.463	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
TP53	7157	broad.mit.edu	37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652		TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	17	GRCh37	CM920675	TP53	M	rs11540652	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152.0	112.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1.0	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	7518263	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.743G>A	17.37:g.7577538C>T	ENSP00000269305:p.Arg248Gln		7518263	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
NACA2	342538	broad.mit.edu	37	17	59668313	59668313	+	Missense_Mutation	SNP	G	G	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr17:59668313G>A	ENST00000521764.1	-	1	250	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	77	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.R77W(1)		large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					ATAGCCTTCCGTGCCCTCTTT	0.463																																																1	Substitution - Missense(1)	ovary(1)	17											247.0	231.0	236.0					17																	59668313		2203	4300	6503	57023095	SO:0001583	missense	342538			BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.229C>T	17.37:g.59668313G>A	ENSP00000427802:p.Arg77Trp		57023095	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.482947	0.63962	.	.	ENSG00000253506	ENST00000521764	T	0.64991	-0.13	0.753	0.753	0.18404	Nascent polypeptide-associated complex NAC (2);	0.000000	0.56097	U	0.000023	T	0.81004	0.4733	H	0.97611	4.04	0.52501	D	0.999953	D	0.89917	1.0	D	0.69479	0.964	T	0.78051	-0.2355	9	.	.	.	.	3.8637	0.09007	0.0:1.0E-4:0.5794:0.4205	.	77	Q9H009	NACA2_HUMAN	W	77	ENSP00000427802:R77W	.	R	-	1	2	NACA2	57023095	1.000000	0.71417	0.992000	0.48379	0.830000	0.47004	2.557000	0.45871	0.702000	0.31825	0.411000	0.27672	CGG		0.463	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
SLC25A19	60386	broad.mit.edu	37	17	73279617	73279617	+	Missense_Mutation	SNP	G	G	A	rs368336055		TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr17:73279617G>A	ENST00000402418.3	-	3	1255	c.346C>T	c.(346-348)Cgg>Tgg	p.R116W	SLC25A19_ENST00000580994.1_Missense_Mutation_p.R116W|SLC25A19_ENST00000416858.2_Missense_Mutation_p.R116W|SLC25A19_ENST00000375261.4_Intron|SLC25A19_ENST00000320362.3_Missense_Mutation_p.R116W|SLC25A19_ENST00000442286.2_Missense_Mutation_p.R116W			Q9HC21	TPC_HUMAN	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	116					deoxynucleotide transport (GO:0030302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	deoxynucleotide transmembrane transporter activity (GO:0030233)	p.R116W(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)			GAGAATTCCCGGGCGTCATAC	0.552																																																1	Substitution - Missense(1)	ovary(1)	17						G	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	55.0	44.0	48.0		346,346,346	2.0	0.0	17		48	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	SLC25A19	NM_021734.4,NM_001126122.1,NM_001126121.1	101,101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	116/321,116/321,116/321	73279617	1,13005	2203	4300	6503	70791212	SO:0001583	missense	60386				CCDS11720.1	17q25.1	2013-05-22	2007-03-08		ENSG00000125454	ENSG00000125454		"""Solute carriers"""	14409	protein-coding gene	gene with protein product		606521	"""solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19"", ""microcephaly, Amish"""	MCPHA		11474176, 11226231, 19798730	Standard	NM_021734		Approved	DNC, MUP1, TPC	uc002jnw.4	Q9HC21		ENST00000402418.3:c.346C>T	17.37:g.73279617G>A	ENSP00000385312:p.Arg116Trp		70791212	E9PF74|Q6V9R7	Missense_Mutation	SNP	ENST00000402418.3	37	CCDS11720.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.490013	0.26686	0.0	1.16E-4	ENSG00000125454	ENST00000416858;ENST00000442286;ENST00000320362;ENST00000402418	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	5.2	1.95	0.26073	Mitochondrial carrier domain (2);	0.477259	0.25941	N	0.027316	T	0.56292	0.1975	N	0.12182	0.205	0.22342	N	0.999183	B	0.13594	0.008	B	0.12837	0.008	T	0.47169	-0.9138	10	0.37606	T	0.19	-4.6711	7.4728	0.27359	0.0724:0.1202:0.6839:0.1236	.	116	Q9HC21	TPC_HUMAN	W	116	ENSP00000397818:R116W;ENSP00000402202:R116W;ENSP00000319574:R116W;ENSP00000385312:R116W	ENSP00000319574:R116W	R	-	1	2	SLC25A19	70791212	0.999000	0.42202	0.002000	0.10522	0.001000	0.01503	2.901000	0.48695	1.189000	0.43028	0.549000	0.68633	CGG		0.552	SLC25A19-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447282.1	NM_021734	
PQLC1	80148	broad.mit.edu	37	18	77710724	77710724	+	Splice_Site	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr18:77710724C>T	ENST00000397778.2	-	2	385	c.203G>A	c.(202-204)tGg>tAg	p.W68*	PQLC1_ENST00000590381.1_Splice_Site_p.W68*|PQLC1_ENST00000357575.4_Splice_Site_p.W68*|PQLC1_ENST00000409073.1_5'UTR	NM_025078.4	NP_079354.2	Q8N2U9	PQLC1_HUMAN	PQ loop repeat containing 1	68	PQ-loop 1.					integral component of membrane (GO:0016021)		p.W68*(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	9		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)		CCCAACTTACCAGAAGAGTAT	0.607																																																1	Substitution - Nonsense(1)	ovary(1)	18											56.0	52.0	54.0					18																	77710724		2203	4299	6502	75811712	SO:0001630	splice_region_variant	80148			AK123870	CCDS12020.1, CCDS54192.1, CCDS54193.1	18q23	2004-01-14			ENSG00000122490	ENSG00000122490			26188	protein-coding gene	gene with protein product						12477932	Standard	NM_025078		Approved	FLJ22378	uc002lnl.2	Q8N2U9	OTTHUMG00000132921	ENST00000397778.2:c.203+1G>A	18.37:g.77710724C>T			75811712	B7Z7D9|G5E989|Q9H6D0	Nonsense_Mutation	SNP	ENST00000397778.2	37	CCDS12020.1	.	.	.	.	.	.	.	.	.	.	C	40	8.010032	0.98607	.	.	ENSG00000122490	ENST00000397778;ENST00000357575;ENST00000351365	.	.	.	5.06	5.06	0.68205	.	0.058319	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.7731	18.4143	0.90563	0.0:1.0:0.0:0.0	.	.	.	.	X	68	.	.	W	-	2	0	PQLC1	75811712	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	7.010000	0.76353	2.327000	0.79052	0.491000	0.48974	TGG		0.607	PQLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256434.1	NM_025078	Nonsense_Mutation
SMARCA4	6597	broad.mit.edu	37	19	11118635	11118635	+	Missense_Mutation	SNP	A	A	G			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr19:11118635A>G	ENST00000429416.3	+	15	2340	c.2059A>G	c.(2059-2061)Aag>Gag	p.K687E	SMARCA4_ENST00000358026.2_Missense_Mutation_p.K687E|SMARCA4_ENST00000444061.3_Missense_Mutation_p.K687E|SMARCA4_ENST00000541122.2_Missense_Mutation_p.K687E|SMARCA4_ENST00000450717.3_Missense_Mutation_p.K687E|SMARCA4_ENST00000413806.3_Missense_Mutation_p.K687E|SMARCA4_ENST00000589677.1_Missense_Mutation_p.K687E|SMARCA4_ENST00000344626.4_Missense_Mutation_p.K687E|SMARCA4_ENST00000590574.1_Missense_Mutation_p.K687E|CTC-215O4.4_ENST00000587831.1_RNA	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	687					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.K687E(1)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CGTGGAGGAGAAGAAGAAGAT	0.587			"""F, N, Mis"""		NSCLC																																		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	2	Substitution - Missense(1)|Unknown(1)	ovary(1)|lung(1)	19											106.0	82.0	90.0					19																	11118635		2203	4300	6503	10979635	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2059A>G	19.37:g.11118635A>G	ENSP00000395654:p.Lys687Glu		10979635	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	9.223	1.033868	0.19590	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14;-2.13;-2.14;-2.14	5.19	5.19	0.71726	.	0.061993	0.64402	D	0.000005	T	0.76579	0.4007	N	0.19112	0.55	0.34576	D	0.71393	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.001;0.001	B;B;B;B;B;B;B	0.06405	0.001;0.002;0.002;0.0;0.002;0.002;0.002	T	0.73665	-0.3911	10	0.09338	T	0.73	-46.9097	14.1702	0.65506	1.0:0.0:0.0:0.0	.	687;687;687;687;687;687;687	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	E	687;687;751;687;687;687;687;687	ENSP00000395654:K687E;ENSP00000350720:K687E;ENSP00000343896:K687E;ENSP00000445036:K687E;ENSP00000392837:K687E;ENSP00000397783:K687E;ENSP00000414727:K687E	ENSP00000343896:K687E	K	+	1	0	SMARCA4	10979635	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.388000	0.59633	2.187000	0.69744	0.459000	0.35465	AAG		0.587	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
CRTC1	23373	broad.mit.edu	37	19	18886579	18886579	+	Silent	SNP	G	G	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr19:18886579G>A	ENST00000321949.8	+	13	1667	c.1641G>A	c.(1639-1641)tcG>tcA	p.S547S	CRTC1_ENST00000594658.1_Silent_p.S506S|CRTC1_ENST00000338797.6_Silent_p.S563S|CRTC1_ENST00000601916.1_Silent_p.S305S	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1									p.S547S(1)	CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						TGCCGGACTCGCAGCAACTGG	0.687																																																1	Substitution - coding silent(1)	ovary(1)	19																																								18747579	SO:0001819	synonymous_variant	23373			AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"""transducer of regulated cAMP response element-binding protein"""	607536	"""mucoepidermoid carcinoma translocated 1"""	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.1641G>A	19.37:g.18886579G>A			18747579		Silent	SNP	ENST00000321949.8	37	CCDS32963.1																																																																																				0.687	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021	
ZNF180	7733	broad.mit.edu	37	19	44980971	44980971	+	Missense_Mutation	SNP	G	G	A	rs567468606		TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr19:44980971G>A	ENST00000221327.4	-	5	2008	c.1727C>T	c.(1726-1728)cCg>cTg	p.P576L	ZNF180_ENST00000592529.1_Missense_Mutation_p.P549L|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.P551L	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	576					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P576L(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				ACATTCATACGGTTTTTCCCC	0.408													G|||	1	0.000199681	0.0	0.0	5008	,	,		21305	0.0		0.0	False		,,,				2504	0.001				Esophageal Squamous(180;1353 2003 32862 46574 49854)											1	Substitution - Missense(1)	ovary(1)	19											104.0	104.0	104.0					19																	44980971		2203	4300	6503	49672811	SO:0001583	missense	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1727C>T	19.37:g.44980971G>A	ENSP00000221327:p.Pro576Leu		49672811	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137100	0.77775	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.56444	0.46;0.46	5.66	5.66	0.87406	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41823	D	0.000812	T	0.70055	0.3180	L	0.56340	1.77	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.71461	-0.4586	10	0.87932	D	0	-14.9646	18.5038	0.90890	0.0:0.0:1.0:0.0	.	551;575;576	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	L	576;551	ENSP00000221327:P576L;ENSP00000375818:P551L	ENSP00000221327:P576L	P	-	2	0	ZNF180	49672811	1.000000	0.71417	0.980000	0.43619	0.876000	0.50452	4.315000	0.59172	2.673000	0.90976	0.591000	0.81541	CCG		0.408	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
TEAD2	8463	broad.mit.edu	37	19	49862705	49862705	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr19:49862705C>T	ENST00000311227.2	-	3	374	c.284G>A	c.(283-285)cGa>cAa	p.R95Q	TEAD2_ENST00000598810.1_Missense_Mutation_p.R95Q|AC010524.4_ENST00000596488.1_RNA|DKKL1_ENST00000594268.1_5'Flank|TEAD2_ENST00000593945.1_Missense_Mutation_p.R95Q|TEAD2_ENST00000377214.4_Missense_Mutation_p.R95Q|TEAD2_ENST00000601519.1_Missense_Mutation_p.R95Q|TEAD2_ENST00000539846.1_5'UTR|TEAD2_ENST00000598397.1_5'Flank	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	95					gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R95Q(2)		central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		TTTTCGAGTTCGGGTCTTCCC	0.507																																																2	Substitution - Missense(2)	ovary(1)|endometrium(1)	19											269.0	223.0	239.0					19																	49862705		2203	4300	6503	54554517	SO:0001583	missense	8463			X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.284G>A	19.37:g.49862705C>T	ENSP00000310701:p.Arg95Gln		54554517	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Missense_Mutation	SNP	ENST00000311227.2	37	CCDS12761.1	.	.	.	.	.	.	.	.	.	.	C	34	5.292965	0.95546	.	.	ENSG00000074219	ENST00000311227;ENST00000377214	T;T	0.64803	-0.12;-0.12	5.27	5.27	0.74061	.	0.000000	0.56097	D	0.000025	T	0.77611	0.4156	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.80764	0.994;0.988	T	0.79732	-0.1680	10	0.87932	D	0	-11.1825	14.7836	0.69784	0.0:1.0:0.0:0.0	.	95;95	Q15562;Q8NA25	TEAD2_HUMAN;.	Q	95	ENSP00000310701:R95Q;ENSP00000366419:R95Q	ENSP00000310701:R95Q	R	-	2	0	TEAD2	54554517	1.000000	0.71417	0.861000	0.33841	0.994000	0.84299	6.745000	0.74860	2.636000	0.89361	0.655000	0.94253	CGA		0.507	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598	
CGREF1	10669	broad.mit.edu	37	2	27324965	27324965	+	Splice_Site	SNP	C	C	T	rs202193679		TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr2:27324965C>T	ENST00000260595.5	-	5	634	c.342G>A	c.(340-342)ccG>ccA	p.P114P	CGREF1_ENST00000402550.1_Splice_Site_p.P114P|CGREF1_ENST00000402394.1_Splice_Site_p.P114P|CGREF1_ENST00000405600.1_Splice_Site_p.P114P|CGREF1_ENST00000404694.3_Splice_Site_p.P236P|CGREF1_ENST00000312734.4_Splice_Site_p.P114P|CGREF1_ENST00000452318.2_Splice_Site_p.P18P			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	114	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.P114P(1)		kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGAGCTTACCGGGTTGGTGG	0.537																																																1	Substitution - coding silent(1)	ovary(1)	2						C	,,,	0,4406		0,0,2203	48.0	50.0	49.0		342,342,54,342	0.9	1.0	2		49	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CGREF1	NM_001166239.1,NM_001166240.1,NM_001166241.1,NM_006569.5	,,,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,,,	114/319,114/133,18/113,114/319	27324965	3,13003	2203	4300	6503	27178469	SO:0001630	splice_region_variant	10669			BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"""EF-hand domain containing"""	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.342+1G>A	2.37:g.27324965C>T			27178469	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Silent	SNP	ENST00000260595.5	37																																																																																					0.537	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569	Silent
HEATR5B	54497	broad.mit.edu	37	2	37227732	37227732	+	Missense_Mutation	SNP	G	G	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr2:37227732G>T	ENST00000233099.5	-	33	5637	c.5542C>A	c.(5542-5544)Cca>Aca	p.P1848T	HEATR5B_ENST00000354531.2_Missense_Mutation_p.P1759T	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1848						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.P1848T(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				AGGTTACCTGGTTGAGAATAT	0.383																																																1	Substitution - Missense(1)	ovary(1)	2											99.0	94.0	96.0					2																	37227732		2203	4300	6503	37081236	SO:0001583	missense	54497			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.5542C>A	2.37:g.37227732G>T	ENSP00000233099:p.Pro1848Thr		37081236	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	7.868	0.727617	0.15439	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.63096	-0.02;-0.02	5.17	5.17	0.71159	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.50171	0.1600	L	0.31476	0.935	0.32233	N	0.573652	B;B	0.02656	0.0;0.0	B;B	0.13407	0.009;0.004	T	0.49380	-0.8946	10	0.09084	T	0.74	.	18.6774	0.91534	0.0:0.0:1.0:0.0	.	1848;1848	Q9P2D3;B9EK47	HTR5B_HUMAN;.	T	1848;1759	ENSP00000233099:P1848T;ENSP00000346531:P1759T	ENSP00000233099:P1848T	P	-	1	0	HEATR5B	37081236	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.676000	0.68131	2.409000	0.81822	0.591000	0.81541	CCA		0.383	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
FANCL	55120	broad.mit.edu	37	2	58449122	58449122	+	Missense_Mutation	SNP	A	A	G			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr2:58449122A>G	ENST00000233741.4	-	5	365	c.329T>C	c.(328-330)tTc>tCc	p.F110S	FANCL_ENST00000540646.1_Missense_Mutation_p.F110S|FANCL_ENST00000403676.1_Intron|FANCL_ENST00000402135.3_Missense_Mutation_p.F110S|FANCL_ENST00000481670.1_5'UTR|FANCL_ENST00000403295.3_Missense_Mutation_p.F110S	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	110	UBC-RWD region (URD).				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|gamete generation (GO:0007276)|protein monoubiquitination (GO:0006513)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F110S(1)		endometrium(1)|large_intestine(1)|lung(4)|ovary(2)	8						GCTTGAGTAGAACTGGGGAGG	0.353								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																																							1	Substitution - Missense(1)	ovary(1)	2											103.0	103.0	103.0					2																	58449122		2203	4300	6503	58302626	SO:0001583	missense	55120	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001197	CCDS1860.1, CCDS46294.1	2p16.1	2014-09-17	2003-10-14	2003-10-15	ENSG00000115392	ENSG00000115392		"""Zinc fingers, PHD-type"", ""Fanconi anemia, complementation groups"""	20748	protein-coding gene	gene with protein product		608111	"""PHD finger protein 9"""	PHF9			Standard	NM_018062		Approved	FLJ10335, FAAP43, Pog	uc002rzx.4	Q9NW38	OTTHUMG00000129349	ENST00000233741.4:c.329T>C	2.37:g.58449122A>G	ENSP00000233741:p.Phe110Ser		58302626	Q6GU60	Missense_Mutation	SNP	ENST00000233741.4	37	CCDS1860.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.763514	0.49574	.	.	ENSG00000115392	ENST00000403295;ENST00000233741;ENST00000402135;ENST00000449070;ENST00000540646	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.4	0.826	0.18829	Fanconi anemia complex, subunit FancL, WD-repeat containing domain (1);	0.108211	0.64402	D	0.000004	T	0.46328	0.1387	L	0.58101	1.795	0.32438	N	0.547105	P;B;D;D	0.60575	0.789;0.056;0.988;0.96	P;B;P;P	0.54312	0.545;0.086;0.709;0.748	T	0.56074	-0.8039	10	0.39692	T	0.17	-11.9476	9.0535	0.36392	0.3948:0.0:0.0:0.6052	.	51;110;110;110	C9JZA9;B5MC31;Q9NW38-2;Q9NW38	.;.;.;FANCL_HUMAN	S	110;110;110;51;110	ENSP00000386097:F110S;ENSP00000233741:F110S;ENSP00000385021:F110S;ENSP00000401280:F51S;ENSP00000441431:F110S	ENSP00000233741:F110S	F	-	2	0	FANCL	58302626	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	1.305000	0.33493	0.390000	0.25115	0.379000	0.24179	TTC		0.353	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062	
POU3F3	5455	broad.mit.edu	37	2	105473036	105473036	+	Silent	SNP	G	G	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr2:105473036G>A	ENST00000361360.2	+	1	1068	c.1068G>A	c.(1066-1068)tcG>tcA	p.S356S	RP11-13J10.1_ENST00000598623.1_RNA	NM_006236.1	NP_006227.1	P20264	PO3F3_HUMAN	POU class 3 homeobox 3	356	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				central nervous system development (GO:0007417)|cerebral cortex radially oriented cell migration (GO:0021799)|forebrain ventricular zone progenitor cell division (GO:0021869)|metanephric ascending thin limb development (GO:0072218)|metanephric DCT cell differentiation (GO:0072240)|metanephric loop of Henle development (GO:0072236)|metanephric macula densa development (GO:0072227)|metanephric thick ascending limb development (GO:0072233)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S356S(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						ACGTGTTCTCGCAGACCACCA	0.612																																																1	Substitution - coding silent(1)	ovary(1)	2											89.0	79.0	83.0					2																	105473036		2203	4300	6503	104839468	SO:0001819	synonymous_variant	5455				CCDS33265.1	2q12.1	2011-06-20	2007-07-13		ENSG00000198914	ENSG00000198914		"""Homeoboxes / POU class"""	9216	protein-coding gene	gene with protein product		602480	"""POU domain class 3, transcription factor 3"""				Standard	NM_006236		Approved	BRN1, OTF8	uc010ywg.2	P20264	OTTHUMG00000153067	ENST00000361360.2:c.1068G>A	2.37:g.105473036G>A			104839468	P78379|Q4ZG25	Silent	SNP	ENST00000361360.2	37	CCDS33265.1																																																																																				0.612	POU3F3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329335.2		
ZC3H6	376940	broad.mit.edu	37	2	113089707	113089707	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr2:113089707C>T	ENST00000409871.1	+	12	3613	c.3212C>T	c.(3211-3213)tCa>tTa	p.S1071L	ZC3H6_ENST00000343936.4_Missense_Mutation_p.S1071L|AC115115.2_ENST00000607612.1_RNA	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1071							metal ion binding (GO:0046872)	p.S1071L(1)		central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						GGAGAAAACTCAAAGAACCAG	0.433																																																1	Substitution - Missense(1)	ovary(1)	2											45.0	42.0	43.0					2																	113089707		1869	4108	5977	112806178	SO:0001583	missense	376940			AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.3212C>T	2.37:g.113089707C>T	ENSP00000386764:p.Ser1071Leu		112806178	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	C	7.158	0.585032	0.13749	.	.	ENSG00000188177	ENST00000409871;ENST00000343936	T;T	0.15017	2.46;2.46	5.33	2.38	0.29361	.	2.194330	0.01585	N	0.021297	T	0.10594	0.0259	N	0.08118	0	0.09310	N	0.999993	B	0.06786	0.001	B	0.04013	0.001	T	0.24225	-1.0166	10	0.62326	D	0.03	0.0299	4.7269	0.12945	0.1149:0.3408:0.4515:0.0929	.	1071	P61129	ZC3H6_HUMAN	L	1071	ENSP00000386764:S1071L;ENSP00000340298:S1071L	ENSP00000340298:S1071L	S	+	2	0	ZC3H6	112806178	0.948000	0.32251	0.670000	0.29842	0.838000	0.47535	1.354000	0.34056	0.575000	0.29434	0.591000	0.81541	TCA		0.433	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
DPP10	57628	broad.mit.edu	37	2	116510801	116510801	+	Silent	SNP	A	A	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	A	A	T	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr2:116510801A>T	ENST00000410059.1	+	11	1482	c.1002A>T	c.(1000-1002)gtA>gtT	p.V334V	DPP10_ENST00000393147.2_Silent_p.V338V|DPP10_ENST00000310323.8_Silent_p.V327V|DPP10_ENST00000409163.1_Silent_p.V284V	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	334						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.V327V(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AGACTGTGGTAAGATGGTTAA	0.358																																																1	Substitution - coding silent(1)	ovary(1)	2											121.0	107.0	112.0					2																	116510801		2203	4300	6503	116227271	SO:0001819	synonymous_variant	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1002A>T	2.37:g.116510801A>T			116227271	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	37	CCDS46400.1																																																																																				0.358	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
TTC21B	79809	broad.mit.edu	37	2	166797568	166797568	+	Missense_Mutation	SNP	C	C	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	A	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr2:166797568C>A	ENST00000243344.7	-	6	816	c.679G>T	c.(679-681)Gat>Tat	p.D227Y	AC010127.5_ENST00000443032.1_RNA|AC010127.5_ENST00000440322.1_RNA	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	227				D -> N (in Ref. 1; BAE45724). {ECO:0000305}.	forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)		p.D227Y(1)		breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						TGGTCCCAATCCTGCAAGGCT	0.388																																																1	Substitution - Missense(1)	ovary(1)	2											107.0	106.0	106.0					2																	166797568		2203	4300	6503	166505814	SO:0001583	missense	79809			AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.679G>T	2.37:g.166797568C>A	ENSP00000243344:p.Asp227Tyr		166505814	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.349038	0.82132	.	.	ENSG00000123607	ENST00000243344	T	0.60424	0.19	5.2	5.2	0.72013	Tetratricopeptide-like helical (1);	0.094053	0.64402	D	0.000001	T	0.80813	0.4695	M	0.89287	3.02	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.986;0.99	D	0.84556	0.0647	10	0.87932	D	0	-18.6507	19.0941	0.93242	0.0:1.0:0.0:0.0	.	227;227	Q7Z4L5-2;Q7Z4L5	.;TT21B_HUMAN	Y	227	ENSP00000243344:D227Y	ENSP00000243344:D227Y	D	-	1	0	TTC21B	166505814	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.926000	0.63433	2.578000	0.87016	0.650000	0.86243	GAT		0.388	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
MN1	4330	broad.mit.edu	37	22	28196333	28196333	+	Missense_Mutation	SNP	G	G	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr22:28196333G>A	ENST00000302326.4	-	1	1153	c.199C>T	c.(199-201)Ccc>Tcc	p.P67S		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	67					intramembranous ossification (GO:0001957)			p.P67S(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						AAGCCGTAGGGCTCCATGTTC	0.682			T	ETV6	"""AML, meningioma"""																																		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	1	Substitution - Missense(1)	ovary(1)	22											35.0	40.0	39.0					22																	28196333		1951	4116	6067	26526333	SO:0001583	missense	4330			X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.199C>T	22.37:g.28196333G>A	ENSP00000304956:p.Pro67Ser		26526333	A9Z1V9	Missense_Mutation	SNP	ENST00000302326.4	37	CCDS42998.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.912180	0.52439	.	.	ENSG00000169184	ENST00000302326	T	0.61859	0.07	4.87	4.87	0.63330	.	0.149412	0.45867	D	0.000322	T	0.56108	0.1963	N	0.19112	0.55	0.44462	D	0.997396	D	0.55605	0.972	P	0.53912	0.737	T	0.58923	-0.7550	10	0.44086	T	0.13	-9.9082	16.9428	0.86222	0.0:0.0:1.0:0.0	.	67	Q10571	MN1_HUMAN	S	67	ENSP00000304956:P67S	ENSP00000304956:P67S	P	-	1	0	MN1	26526333	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	6.423000	0.73361	2.400000	0.81607	0.561000	0.74099	CCC		0.682	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
EBLN2	55096	broad.mit.edu	37	3	73111514	73111514	+	Silent	SNP	A	A	G			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr3:73111514A>G	ENST00000533473.1	+	1	705	c.282A>G	c.(280-282)caA>caG	p.Q94Q	PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	94										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						TGGAACCCCAACCCAGCATTG	0.463																																																0			3											38.0	36.0	37.0					3																	73111514		1923	4117	6040	73194204	SO:0001819	synonymous_variant	55096				CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"""endogenous Borna-like N element 2"""	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.282A>G	3.37:g.73111514A>G			73194204	Q8WWH3|Q9NW89	Silent	SNP	ENST00000533473.1	37	CCDS54608.1																																																																																				0.463	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029	
OTOP1	133060	broad.mit.edu	37	4	4199527	4199527	+	Missense_Mutation	SNP	G	G	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr4:4199527G>A	ENST00000296358.4	-	5	1058	c.1034C>T	c.(1033-1035)tCg>tTg	p.S345L		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	345					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.S345L(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GATGAGTGCCGACTCGCTCTT	0.572																																																1	Substitution - Missense(1)	ovary(1)	4											50.0	49.0	49.0					4																	4199527		2203	4300	6503	4250428	SO:0001583	missense	133060			BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1034C>T	4.37:g.4199527G>A	ENSP00000296358:p.Ser345Leu		4250428	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	7.641	0.680814	0.14907	.	.	ENSG00000163982	ENST00000296358	T	0.19250	2.16	4.8	3.06	0.35304	.	0.533330	0.19534	N	0.111964	T	0.10809	0.0264	N	0.12471	0.22	0.31646	N	0.647446	B	0.23316	0.083	B	0.18871	0.023	T	0.11227	-1.0596	10	0.36615	T	0.2	-14.2535	7.9361	0.29931	0.3488:0.0:0.6512:0.0	.	345	Q7RTM1	OTOP1_HUMAN	L	345	ENSP00000296358:S345L	ENSP00000296358:S345L	S	-	2	0	OTOP1	4250428	0.897000	0.30589	0.862000	0.33874	0.271000	0.26615	1.457000	0.35212	0.557000	0.29117	0.404000	0.27445	TCG		0.572	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
LNX1	84708	broad.mit.edu	37	4	54424124	54424124	+	Intron	SNP	C	C	T	rs200583618		TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr4:54424124C>T	ENST00000263925.7	-	2	695				LNX1_ENST00000306888.2_Silent_p.A3A|FIP1L1_ENST00000507166.1_Intron	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase						protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A3A(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			GCAACAGAAGCGCCTTCATTC	0.532																																																1	Substitution - coding silent(1)	ovary(1)	4						T	,	0,4406		0,0,2203	169.0	141.0	150.0		,9	0.6	1.0	4		150	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous	LNX1	NM_001126328.1,NM_032622.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	,3/633	54424124	1,13005	2203	4300	6503	54118881	SO:0001627	intron_variant	84708			AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"""RING-type (C3HC4) zinc fingers"""	6657	protein-coding gene	gene with protein product		609732	"""ligand of numb-protein X"", ""ligand of numb-protein X 1"""	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.380+15665G>A	4.37:g.54424124C>T			54118881	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Silent	SNP	ENST00000263925.7	37	CCDS47057.1																																																																																				0.532	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2		
DDIT4L	115265	broad.mit.edu	37	4	101108838	101108838	+	Missense_Mutation	SNP	G	G	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr4:101108838G>A	ENST00000273990.2	-	3	792	c.578C>T	c.(577-579)tCc>tTc	p.S193F	RP11-588P8.1_ENST00000515782.1_RNA|RP11-15B17.1_ENST00000515026.1_RNA	NM_145244.3	NP_660287.1	Q96D03	DDT4L_HUMAN	DNA-damage-inducible transcript 4-like	193					negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)		p.S193F(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(2)	12				OV - Ovarian serous cystadenocarcinoma(123;5.75e-09)		CCCTTTTTAGGACCCTTCAAT	0.378																																																1	Substitution - Missense(1)	ovary(1)	4											40.0	45.0	43.0					4																	101108838		2202	4298	6500	101327861	SO:0001583	missense	115265			BC013592	CCDS34036.1	4q23	2008-02-05				ENSG00000145358			30555	protein-coding gene	gene with protein product	"""regulated in development and DNA damage response 2"", "" similar to Smhs1 protein"""	607730				12477932	Standard	NM_145244		Approved	REDD2, Rtp801L	uc003hvq.3	Q96D03		ENST00000273990.2:c.578C>T	4.37:g.101108838G>A	ENSP00000354830:p.Ser193Phe		101327861	B2R7C3	Missense_Mutation	SNP	ENST00000273990.2	37	CCDS34036.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.397650	0.42512	.	.	ENSG00000145358	ENST00000273990	T	0.47177	0.85	5.86	4.12	0.48240	.	0.287924	0.39210	N	0.001421	T	0.28300	0.0699	N	0.08118	0	0.26738	N	0.970455	B	0.12630	0.006	B	0.15052	0.012	T	0.24476	-1.0159	10	0.87932	D	0	-8.9248	10.9982	0.47589	0.0:0.7918:0.1355:0.0727	.	193	Q96D03	DDT4L_HUMAN	F	193	ENSP00000354830:S193F	ENSP00000354830:S193F	S	-	2	0	DDIT4L	101327861	1.000000	0.71417	0.960000	0.40013	0.685000	0.39939	2.157000	0.42320	0.803000	0.34113	-0.165000	0.13383	TCC		0.378	DDIT4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363423.1	NM_145244	
TSSK1B	83942	broad.mit.edu	37	5	112769842	112769842	+	Missense_Mutation	SNP	C	C	T	rs192780356	byFrequency	TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr5:112769842C>T	ENST00000390666.3	-	1	886	c.695G>A	c.(694-696)cGc>cAc	p.R232H	MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000510381.2_RNA|CTD-2201G3.1_ENST00000416046.2_RNA|CTD-2201G3.1_ENST00000383058.4_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	232	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.R232H(1)|p.R232L(1)		large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		GAAGTTGACGCGGTGCTCCTT	0.587													C|||	4	0.000798722	0.0015	0.0	5008	,	,		21332	0.0		0.0	False		,,,				2504	0.002															2	Substitution - Missense(2)	ovary(1)|lung(1)	5											81.0	74.0	76.0					5																	112769842		2202	4300	6502	112797741	SO:0001583	missense	83942			AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"""serine/threonine kinase 22D (spermiogenesis associated)"", ""testis-specific serine kinase 1"""	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.695G>A	5.37:g.112769842C>T	ENSP00000375081:p.Arg232His		112797741	B2R8D9	Missense_Mutation	SNP	ENST00000390666.3	37	CCDS4112.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	2.627	-0.287221	0.05605	.	.	ENSG00000212122	ENST00000390666	T	0.66099	-0.19	0.9	0.9	0.19278	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.34555	U	0.003870	T	0.44561	0.1299	L	0.27053	0.805	0.09310	N	1	P	0.41710	0.76	B	0.41646	0.362	T	0.38585	-0.9654	10	0.87932	D	0	.	4.9573	0.14048	0.0:1.0:0.0:0.0	.	232	Q9BXA7	TSSK1_HUMAN	H	232	ENSP00000375081:R232H	ENSP00000375081:R232H	R	-	2	0	TSSK1B	112797741	0.000000	0.05858	0.527000	0.27925	0.126000	0.20510	0.432000	0.21461	0.308000	0.22923	0.313000	0.20887	CGC		0.587	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028	
PCDHA4	56144	broad.mit.edu	37	5	140186856	140186856	+	Silent	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr5:140186856C>T	ENST00000530339.1	+	1	84	c.84C>T	c.(82-84)aaC>aaT	p.N28N	PCDHA4_ENST00000512229.2_Silent_p.N28N|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_Silent_p.N28N	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	28					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.N28N(1)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGCAGGGAACGGTCAGCTCC	0.627																																																1	Substitution - coding silent(1)	ovary(1)	5											64.0	71.0	69.0					5																	140186856		2203	4300	6503	140167040	SO:0001819	synonymous_variant	56144			AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.84C>T	5.37:g.140186856C>T			140167040	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																				0.627	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
GABRG2	2566	broad.mit.edu	37	5	161576234	161576234	+	Missense_Mutation	SNP	C	C	G			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	G	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr5:161576234C>G	ENST00000361925.4	+	8	1263	c.1043C>G	c.(1042-1044)tCt>tGt	p.S348C	GABRG2_ENST00000414552.2_Missense_Mutation_p.S388C|GABRG2_ENST00000356592.3_Missense_Mutation_p.S348C|GABRG2_ENST00000393933.4_Missense_Mutation_p.S253C			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	348					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S348C(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTTGTCTTCTCTGCTCTGGTG	0.443																																																1	Substitution - Missense(1)	ovary(1)	5											237.0	195.0	209.0					5																	161576234		2203	4300	6503	161508812	SO:0001583	missense	2566				CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1043C>G	5.37:g.161576234C>G	ENSP00000354651:p.Ser348Cys		161508812	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	37	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.929532	0.52759	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11	5.61	5.61	0.85477	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.051120	0.85682	D	0.000000	D	0.84960	0.5588	N	0.05199	-0.095	0.54753	D	0.999982	P;B;B	0.46912	0.886;0.0;0.0	P;B;B	0.55999	0.789;0.004;0.004	D	0.87401	0.2369	10	0.49607	T	0.09	.	19.6572	0.95847	0.0:1.0:0.0:0.0	.	388;348;348	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	C	348;388;348;253	ENSP00000349000:S348C;ENSP00000410732:S388C;ENSP00000354651:S348C;ENSP00000377510:S253C	ENSP00000349000:S348C	S	+	2	0	GABRG2	161508812	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.726000	0.84824	2.630000	0.89119	0.650000	0.86243	TCT		0.443	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1		
BBS9	27241	broad.mit.edu	37	7	33195288	33195288	+	Missense_Mutation	SNP	G	G	A			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr7:33195288G>A	ENST00000242067.6	+	4	823	c.302G>A	c.(301-303)aGa>aAa	p.R101K	BBS9_ENST00000354265.4_Missense_Mutation_p.R101K|BBS9_ENST00000350941.3_Missense_Mutation_p.R101K|BBS9_ENST00000425508.2_Missense_Mutation_p.R56K|BBS9_ENST00000396127.2_Missense_Mutation_p.R101K|BBS9_ENST00000355070.2_Missense_Mutation_p.R101K	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	101					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.R101K(1)	BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			TTACATTCTAGAAAACTTTGT	0.303									Bardet-Biedl syndrome																																							1	Substitution - Missense(1)	ovary(1)	7											84.0	81.0	82.0					7																	33195288		2202	4298	6500	33161813	SO:0001583	missense	27241	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"""parathyroid hormone responsive B1 gene"""	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.302G>A	7.37:g.33195288G>A	ENSP00000242067:p.Arg101Lys		33161813	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Missense_Mutation	SNP	ENST00000242067.6	37	CCDS43566.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.972115	0.74246	.	.	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132;ENST00000396125;ENST00000425508	D;D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65;-1.65	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	D	0.82300	0.5007	L	0.50847	1.595	0.35106	D	0.765748	P;B;P;B;B	0.41450	0.75;0.174;0.51;0.174;0.174	B;B;P;B;B	0.47015	0.217;0.163;0.534;0.163;0.336	D	0.85338	0.1094	9	.	.	.	-20.7266	13.1415	0.59438	0.0805:0.0:0.9195:0.0	.	101;101;101;101;101	B3KQ86;Q3SYG4-2;E9PDC9;Q3SYG4-4;Q3SYG4	.;.;.;.;PTHB1_HUMAN	K	101;101;101;101;101;101;101;56	ENSP00000242067:R101K;ENSP00000313122:R101K;ENSP00000379433:R101K;ENSP00000347182:R101K;ENSP00000346214:R101K;ENSP00000405151:R56K	.	R	+	2	0	BBS9	33161813	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	6.182000	0.71995	2.682000	0.91365	0.557000	0.71058	AGA		0.303	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1		
EBF2	64641	broad.mit.edu	37	8	25718648	25718648	+	Missense_Mutation	SNP	G	G	A	rs371873709		TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr8:25718648G>A	ENST00000520164.1	-	13	1796	c.1259C>T	c.(1258-1260)gCg>gTg	p.A420V	EBF2_ENST00000408929.3_Missense_Mutation_p.A272V|EBF2_ENST00000535548.1_Missense_Mutation_p.A151V	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	420					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A420V(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GCCACTGTGCGCTGGGGAGCT	0.522																																					Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)											1	Substitution - Missense(1)	ovary(1)	8						G	VAL/ALA	1,4055		0,1,2027	112.0	117.0	115.0		1259	5.3	1.0	8		115	0,8386		0,0,4193	no	missense	EBF2	NM_022659.2	64	0,1,6220	AA,AG,GG		0.0,0.0247,0.0080	benign	420/576	25718648	1,12441	2028	4193	6221	25774565	SO:0001583	missense	64641			AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.1259C>T	8.37:g.25718648G>A	ENSP00000430241:p.Ala420Val		25774565	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	37	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	G	2.706	-0.269788	0.05716	2.47E-4	0.0	ENSG00000221818	ENST00000520164;ENST00000408929;ENST00000535548	T;T;T	0.40756	1.02;1.02;1.02	5.29	5.29	0.74685	.	0.097978	0.64402	D	0.000001	T	0.21468	0.0517	N	0.04203	-0.255	0.50467	D	0.999876	B	0.09022	0.002	B	0.08055	0.003	T	0.09079	-1.0691	10	0.25106	T	0.35	-4.7849	12.3066	0.54906	0.0775:0.0:0.9224:0.0	.	420	Q9HAK2	COE2_HUMAN	V	420;272;151	ENSP00000430241:A420V;ENSP00000386178:A272V;ENSP00000437909:A151V	ENSP00000386178:A272V	A	-	2	0	EBF2	25774565	1.000000	0.71417	1.000000	0.80357	0.049000	0.14656	5.534000	0.67167	2.476000	0.83614	0.655000	0.94253	GCG		0.522	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659	
ADAMTSL2	9719	broad.mit.edu	37	9	136412308	136412308	+	Silent	SNP	G	G	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr9:136412308G>T	ENST00000354484.4	+	9	1469	c.912G>T	c.(910-912)ggG>ggT	p.G304G	ADAMTSL2_ENST00000393061.3_Silent_p.G413G|ADAMTSL2_ENST00000393060.1_Silent_p.G304G	NM_001145320.1	NP_001138792.1	Q86TH1	ATL2_HUMAN	ADAMTS-like 2	304					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G304G(1)		kidney(2)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(145;9.31e-08)|Epithelial(140;6.62e-07)|all cancers(34;7.74e-06)		TGGCACAGGGGCCCACCAACC	0.617																																																1	Substitution - coding silent(1)	ovary(1)	9											133.0	128.0	130.0					9																	136412308		2203	4300	6503	135402129	SO:0001819	synonymous_variant	9719			AB011177	CCDS6976.1	9q34.3	2005-01-12			ENSG00000197859	ENSG00000197859			14631	protein-coding gene	gene with protein product		612277				9628581, 14667842	Standard	NM_014694		Approved	KIAA0605	uc004cei.3	Q86TH1	OTTHUMG00000131706	ENST00000354484.4:c.912G>T	9.37:g.136412308G>T			135402129	B1B0D5|O60345	Silent	SNP	ENST00000354484.4	37	CCDS6976.1																																																																																				0.617	ADAMTSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254619.1	NM_014694	
MAGED2	10916	broad.mit.edu	37	X	54836543	54836543	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chrX:54836543C>T	ENST00000375068.1	+	3	667	c.434C>T	c.(433-435)cCc>cTc	p.P145L	MAGED2_ENST00000375058.1_Missense_Mutation_p.P145L|MAGED2_ENST00000396224.1_Missense_Mutation_p.P145L|MAGED2_ENST00000375060.1_Missense_Mutation_p.P107L|MAGED2_ENST00000497484.1_3'UTR|MAGED2_ENST00000375062.4_Missense_Mutation_p.P107L|MAGED2_ENST00000347546.4_Missense_Mutation_p.P127L|MAGED2_ENST00000218439.4_Missense_Mutation_p.P145L|MAGED2_ENST00000375053.2_Missense_Mutation_p.P145L			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	145						membrane (GO:0016020)		p.P145L(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						GAGGCTGCACCCTCTCAGGCC	0.562																																																1	Substitution - Missense(1)	ovary(1)	X											16.0	15.0	15.0					X																	54836543		2202	4298	6500	54853268	SO:0001583	missense	10916			AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated protein"", ""breast cancer associated gene 1"", ""melanoma-associated antigen D2"", ""hepatocellular carcinoma-associated protein HCA10"""	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.434C>T	X.37:g.54836543C>T	ENSP00000364209:p.Pro145Leu		54853268	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	37	CCDS14362.1	.	.	.	.	.	.	.	.	.	.	C	4.124	0.021241	0.08006	.	.	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.71698	1.02;1.02;4.24;-0.59;1.02;1.02;1.02;1.02;1.02	4.36	3.5	0.40072	.	0.440715	0.19425	N	0.114591	T	0.46678	0.1405	N	0.08118	0	0.23889	N	0.996552	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.32107	-0.9919	10	0.39692	T	0.17	.	6.9881	0.24739	0.0:0.8759:0.0:0.1241	.	127;107;145	Q9UNF1-2;Q5H907;Q9UNF1	.;.;MAGD2_HUMAN	L	145;145;89;127;107;145;145;107;145	ENSP00000364209:P145L;ENSP00000364193:P145L;ENSP00000336962:P89L;ENSP00000340290:P127L;ENSP00000364202:P107L;ENSP00000218439:P145L;ENSP00000364198:P145L;ENSP00000364200:P107L;ENSP00000379526:P145L	ENSP00000218439:P145L	P	+	2	0	MAGED2	54853268	0.987000	0.35691	0.721000	0.30653	0.082000	0.17680	0.556000	0.23438	1.177000	0.42855	0.600000	0.82982	CCC		0.562	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599	
IRS4	8471	broad.mit.edu	37	X	107977383	107977383	+	Missense_Mutation	SNP	C	C	T			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chrX:107977383C>T	ENST00000372129.2	-	1	2268	c.2192G>A	c.(2191-2193)cGc>cAc	p.R731H	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	731	CRK-binding.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.R731H(1)		NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TCGAGAGTGGCGCTTTTTTGA	0.512																																																1	Substitution - Missense(1)	ovary(1)	X											70.0	71.0	71.0					X																	107977383		2203	4300	6503	107864039	SO:0001583	missense	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.2192G>A	X.37:g.107977383C>T	ENSP00000361202:p.Arg731His		107864039		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	C	6.944	0.543989	0.13312	.	.	ENSG00000133124	ENST00000372129	T	0.21031	2.03	5.33	-2.14	0.07123	.	0.420142	0.23596	N	0.046485	T	0.09335	0.0230	L	0.31294	0.92	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.17623	-1.0363	10	0.23302	T	0.38	-0.2394	0.9316	0.01336	0.3551:0.1457:0.1152:0.3841	.	731	O14654	IRS4_HUMAN	H	731	ENSP00000361202:R731H	ENSP00000361202:R731H	R	-	2	0	IRS4	107864039	0.021000	0.18746	0.005000	0.12908	0.969000	0.65631	-0.237000	0.08990	-0.253000	0.09514	0.600000	0.82982	CGC		0.512	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
TRIT1	54802	broad.mit.edu	37	1	40315884	40315884	+	Frame_Shift_Del	DEL	G	G	-			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	G	G	-	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr1:40315884delG	ENST00000316891.5	-	5	624	c.610delC	c.(610-612)catfs	p.H204fs	TRIT1_ENST00000545233.1_5'UTR|TRIT1_ENST00000541099.1_Intron|TRIT1_ENST00000372818.1_Frame_Shift_Del_p.H204fs|TRIT1_ENST00000537440.1_5'UTR|TRIT1_ENST00000537223.1_Intron|TRIT1_ENST00000441669.2_Frame_Shift_Del_p.H124fs|TRIT1_ENST00000491865.1_Intron	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	204					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)	p.H204fs*16(1)		breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TGTTGACGATGGAGAAATTCA	0.463																																																1	Deletion - Frameshift(1)	ovary(1)	1											79.0	76.0	77.0					1																	40315884		2203	4300	6503	40088471	SO:0001589	frameshift_variant	54802			AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	2.5.1.8		20286	protein-coding gene	gene with protein product						11111046, 15870694	Standard	NM_017646		Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.610delC	1.37:g.40315884delG	ENSP00000321810:p.His204fs		40088471	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	Frame_Shift_Del	DEL	ENST00000316891.5	37	CCDS30681.1																																																																																				0.463	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025627.2	NM_017646	
SLC30A1	7779	broad.mit.edu	37	1	211749236	211749242	+	Frame_Shift_Del	DEL	CAGATTC	CAGATTC	-			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	CAGATTC	CAGATTC	-	-	CAGATTC	CAGATTC	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chr1:211749236_211749242delCAGATTC	ENST00000367001.4	-	2	1141_1147	c.1012_1018delGAATCTG	c.(1012-1020)gaatctgctfs	p.ESA338fs		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	338					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)	p.E338fs*17(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		AGAATAAGAGCAGATTCCTTAAGTAAT	0.338																																																1	Deletion - Frameshift(1)	ovary(1)	1																																								209815865	SO:0001589	frameshift_variant	7779			AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"""Solute carriers"""	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.1012_1018delGAATCTG	1.37:g.211749236_211749242delCAGATTC	ENSP00000355968:p.Glu338fs		209815859	Q0VAK9|Q9BZF6	Frame_Shift_Del	DEL	ENST00000367001.4	37	CCDS1499.1																																																																																				0.338	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2		
ARHGAP36	158763	broad.mit.edu	37	X	130215886	130215889	+	Frame_Shift_Del	DEL	GACA	GACA	-			TCGA-24-2260-01A-01W-0722-08	TCGA-24-2260-11A-01W-0722-08	GACA	GACA	-	-	GACA	GACA	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	efe741eb-7ce2-4d6c-b852-8598413c649e	fef5b503-2b89-41e6-80b2-cc70c511d762	g.chrX:130215886_130215889delGACA	ENST00000276211.5	+	2	592_595	c.247_250delGACA	c.(247-252)gacagafs	p.DR83fs	ARHGAP36_ENST00000370922.1_Frame_Shift_Del_p.DR71fs|ARHGAP36_ENST00000370921.1_5'Flank	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	83					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.D83fs*16(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						ATTCAAACCTGACAGAGGTAAGCT	0.598																																																1	Deletion - Frameshift(1)	ovary(1)	X																																								130043570	SO:0001589	frameshift_variant	158763				CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"""Rho GTPase activating proteins"""	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.247_250delGACA	X.37:g.130215886_130215889delGACA	ENSP00000276211:p.Asp83fs		130043567	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Frame_Shift_Del	DEL	ENST00000276211.5	37	CCDS14628.1																																																																																				0.598	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967	
